AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_hpyl_reg_300.orf -o216_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00546	21	AE000511
#2	RHP00549	16	AE000511
#3	RHP00550	73	AE000511
#4	RHP00552	130	AE000511
#5	RHP01673	21	AE000511
#6	RHP00716	174	AE000511

Motif number 1

        GGTTTTGTGAGGTTAA         	2	3	1	TTTTGGGTTA	    0.986429	-14
TTTAAGCATGTTTTGGGTGCTTTTGTTGTATAA	3	13	1	TTTTGGGTTT	     0.97416	-61
TTCGTATTAAATTTGAGATTATACAACAAAAGC	3	31	0	ATTTGGTATA	    0.898847	-43
AATACGAATATTTTAGGAGATTTTTGTA     	3	56	1	TTTTAGGTTT	    0.978645	-18
ATCCTTTTTAATTTAAATGCTTTGTTGTATAAT	4	17	1	ATTTAAGTTT	    0.801173	-114
TTGCGTATTTTTTCAAAATTATACAACAAAGCA	4	34	0	TTTCAATATA	    0.696712	-97
CGCCTTTTGCTTTTACGCTTTTAATTGTTGCGT	4	61	0	TTTTAGTTTA	    0.987058	-70
GAACGCTCTATTTTAGGATAATA          	4	118	1	TTTTAGTATA	    0.964093	-13
TGTTTAAAAAATTAGGGTTTTTAAGTAGAAGGT	6	97	1	ATTAGGTTTA	    0.778607	-78
AGGTATAAGAGTTTATGCTATTTTTTTAAGGTT	6	126	1	GTTTAGTTTT	    0.902373	-49
TATGCTATTTTTTTAAGGTTTTAAAATCAAATT	6	139	1	TTTTAGTTTA	    0.987058	-36
TAAAATCAAATTTCAAAGGATTAGC        	6	160	1	TTTCAAGTTA	    0.882159	-15
          ***** * * ***

Masking position 3
Map Score:   12.7146

Number of sites scoring better than the average of aligned sites = 2009
Number in coding regions = 1675
Number in noncoding regions = 334
Number of orfs with sites within 600 bp upstream = 225
Fraction of orfs with sites within 600 bp upstream = 0.0361388


Motif number 2

          CTTTTAAGCATGTTTTGGGT	3	1	1	CTTTTAAGCA	    0.939492	-73
TTGGGTGCTTTTGTTGTATAATCTCAAATT	3	25	1	TTGTTGTATA	    0.830679	-49
TTTAAATGCTTTGTTGTATAATTTTGAAAA	4	28	1	TTGTTGTATA	    0.830679	-103
ACGCTTTTAATTGTTGCGTATTTTTTCAAA	4	50	0	TTGTTGCGTA	    0.968889	-81
ACGCCTTTTGCTTTTACGCTTTTAATTGTT	4	65	0	CTTTTACGCT	     0.79079	-66
ATCCAACCATTTTTTAAGGAACGCTCTATT	4	100	1	TTTTTAAGGA	    0.942863	-31
AAGAAAATTCTTGTTGCGAACGGATAATAA	6	37	1	TTGTTGCGAA	    0.884831	-138
TAATAACCCTCTTTTGTGTAAAAATTGTGG	6	61	1	CTTTTGTGTA	    0.929895	-114
AAACCCTAATTTTTTAAACACCATTTCCAC	6	87	0	TTTTTAAACA	     0.82667	-88
AAAATTAGGGTTTTTAAGTAGAAGGTATAA	6	104	1	TTTTTAAGTA	    0.960278	-71
TTATGCTATTTTTTTAAGGTTTTAAAATCA	6	138	1	TTTTTAAGGT	    0.808631	-37
          **********

Masking position 5
Map Score:   8.63274

Number of sites scoring better than the average of aligned sites = 1105
Number in coding regions = 958
Number in noncoding regions = 147
Number of orfs with sites within 600 bp upstream = 134
Fraction of orfs with sites within 600 bp upstream = 0.0215226


Motif number 3

     TGGACTATCCTTTTTAATTTAAATG	4	6	1	TATCCTTTTT	    0.924134	-125
TTTTAATTTAAATGCTTTGTTGTATAATTT	4	22	1	AATGCTTTGT	    0.929326	-109
CTTTTGCTTTTACGCTTTTAATTGTTGCGT	4	61	0	TACGCTTTTA	    0.891616	-70
TTGGATTTGGAACGCCTTTTGCTTTTACGC	4	76	0	AACGCCTTTT	    0.969645	-55
TTCCAAATCCAACCATTTTTTAAGGAACGC	4	94	1	AACCATTTTT	    0.867668	-37
TTTTTTAAGGAACGCTCTATTTTAGGATAA	4	109	1	AACGCTCTAT	    0.881382	-22
AACGGATAATAACCCTCTTTTGTGTAAAAA	6	55	1	AACCCTCTTT	    0.979217	-120
TAATTTTTTAAACACCATTTCCACAATTTT	6	81	0	AACACCATTT	    0.721645	-94
TCTACTTAAAAACCCTAATTTTTTAAACAC	6	96	0	AACCCTAATT	    0.847279	-79
TATAAGAGTTTATGCTATTTTTTTAAGGTT	6	129	1	TATGCTATTT	    0.864677	-46
       GCTAATCCTTTGAAATTTGATTT	6	162	0	AATCCTTTGA	     0.76541	-13
          **********

Masking position 2
Map Score:   8.85226

Number of sites scoring better than the average of aligned sites = 3542
Number in coding regions = 3057
Number in noncoding regions = 485
Number of orfs with sites within 600 bp upstream = 291
Fraction of orfs with sites within 600 bp upstream = 0.0467395


Motif number 4

         GTGTTTTCCTTAATGTCAATT	1	11	0	TGTTTTCCTT	    0.957704	-11
        TGGACTATCCTTTTTAATTTAA	4	3	1	GACTATCCTT	    0.933351	-128
          TATTATCCTAAAATAGAGCG	4	121	0	TATTATCCTA	     0.97933	-10
AGAATTTTCTTGTTATCTTAATGTAAAGGT	6	18	0	TGTTATCTTA	    0.908759	-157
AAAAGAGGGTTATTATCCGTTCGCAACAAG	6	46	0	TATTATCCGT	    0.968834	-129
          **********

Masking position 6
Map Score:   0.803182

Number of sites scoring better than the average of aligned sites = 156
Number in coding regions = 113
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 5

          **********

No masking
Map Score:   6.84553e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   6.84553e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   6.84553e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0